524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()

613
(12 years ago)
by stehr:
Changed behaviour of graphAverager: Now evaluating consensus threshold based only on edges that could really exist (i.e. both ends map to non-gaps) rather than simple count of templates. The old behaviour can be restored (for comparison) by setting legacyMode=true in getAverageGraph() and getConsensusGraph().

639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.

517
(12 years ago)
by duarte:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this.
NOTE: graph averaging hasn't been tested after the change

575
(12 years ago)
by filippis:
reconstruct:
-rmsd to mirrored pdb has been added in the report file
Pdb:
-comment for outputing missing atoms added
PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added

576
(12 years ago)
by filippis:
RIGraph:Now you can store unweighted graphs in db and also select the db that contains the ids for the single models.
-paramater weighted added to write_graph_to_db and write_graph_to_db_fast methods. If true, it works as before (atomWeight is written to db field weight) else the db field weight gets always value 1. Methods without this parameter still exist and work as before.
-protected field singleModelsDb and corresponding methods getSingleModelsDb and setSingleModelsDb have been added. All constructors set the singleModelsDb field to DEFAULT_SINGLEMODELS_DB which equals to "ioannis". Changes have been also made to write_graph_to_db and write_graph_to_db_fast methods to deal with the singleModelsDb field.
DbRIGraph, testDbRIGraph:Changes have been also made to address the reading of (un)weighted graphs from db.
doClassifySingleModels.sh has been added. You can create your own table with ids for the single models wherever you want.
createGraphDs.sh: mode to drop tables has been added.

609
(12 years ago)
by duarte:
Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

609
(12 years ago)
by duarte:
Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

609
(12 years ago)
by duarte:
Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph

609
(12 years ago)
by duarte:
Extracted constant NULL_CHAIN_CODE that was still hard-coded in MANY places. Now should be safe to replace the value of the constant from "NULL" to something else.
Using TemplateList.readIdsListFile() in averageGraph, dumpseq and genGraph so that is now a standard way of reading list files with pdbcodes/chaincodes.
NOTE: this introduces an incompatibility with legacy list files: we can't read a NULL pdb chain code with the "NULL" string e.g. '1i1b NULL'. This is fine because since PDB-REMEDIATED all NULL chains are now "A".
Fixed a few things and made more standard the scripts dumpseq and genGraph